Merge pull request #4470 from akohlmey/bye-bye-python-zwei

Remove support for Python 2.x and show corresponding errors.

cmake/CMakeLists.txt

@@ -225,6 +225,12 @@ if(DEFINED ENV{VIRTUAL_ENV} AND NOT Python_EXECUTABLE)
     "   Setting Python interpreter to: ${Python_EXECUTABLE}")
 endif()
 
+find_package(Python COMPONENTS Interpreter QUIET)
+# NOTE: RHEL 8.0 and Ubuntu 18.04LTS ship with Python 3.6, Python 3.8 was EOL in 2024
+if(Python_VERSION VERSION_LESS 3.6)
+  message(FATAL_ERROR "LAMMPS requires Python 3.6 or later")
+endif()
+
 set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
 mark_as_advanced(LAMMPS_MACHINE)
 if(LAMMPS_MACHINE)

cmake/Modules/CodingStandard.cmake

@@ -1,40 +1,39 @@
-# use default (or custom) Python executable, if version is sufficient
+# use default (or custom) Python executable.
-if(Python_VERSION VERSION_GREATER_EQUAL 3.6)
+# Python version check is in main CMakeLists.txt file
+if(Python_EXECUTABLE)
   set(Python3_EXECUTABLE ${Python_EXECUTABLE})
 endif()
 find_package(Python3 COMPONENTS Interpreter)
 
 if(Python3_EXECUTABLE)
-    if(Python3_VERSION VERSION_GREATER_EQUAL 3.6)
+  add_custom_target(
-        add_custom_target(
+    check-whitespace
-          check-whitespace
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Check for whitespace errors")
-          COMMENT "Check for whitespace errors")
+  add_custom_target(
-        add_custom_target(
+    check-homepage
-          check-homepage
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Check for homepage URL errors")
-          COMMENT "Check for homepage URL errors")
+  add_custom_target(
-        add_custom_target(
+    check-permissions
-          check-permissions
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Check for permission errors")
-          COMMENT "Check for permission errors")
+  add_custom_target(
-        add_custom_target(
+    fix-whitespace
-          fix-whitespace
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Fix whitespace errors")
-          COMMENT "Fix whitespace errors")
+  add_custom_target(
-        add_custom_target(
+    fix-homepage
-          fix-homepage
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Fix homepage URL errors")
-          COMMENT "Fix homepage URL errors")
+  add_custom_target(
-        add_custom_target(
+    fix-permissions
-          fix-permissions
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Fix permission errors")
-          COMMENT "Fix permission errors")
-    endif()
 endif()

cmake/Modules/Packages/ML-IAP.cmake

@@ -24,9 +24,7 @@ if(MLIAP_ENABLE_PYTHON)
   if(NOT PKG_PYTHON)
     message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
   endif()
-  if(Python_VERSION VERSION_LESS 3.6)
+  # Python version check is in main CMakeLists.txt file
-    message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
-  endif()
 
   set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
   file(GLOB MLIAP_CYTHON_SRC CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)

doc/src/Build_extras.rst

@@ -1139,11 +1139,10 @@ POEMS package
 PYTHON package
 ---------------------------
 
-Building with the PYTHON package requires you have a the Python development
+Building with the PYTHON package requires you have a the Python
-headers and library available on your system, which needs to be a Python 2.7
+development headers and library available on your system, which
-version or a Python 3.x version.  Since support for Python 2.x has ended,
+needs to be Python version 3.6 or later.  See ``lib/python/README``
-using Python 3.x is strongly recommended. See ``lib/python/README`` for
+for additional details.
-additional details.
 
 .. tabs::
 
@@ -1159,7 +1158,7 @@ additional details.
       set the Python_EXECUTABLE variable to specify which Python
       interpreter should be used.  Note note that you will also need to
       have the development headers installed for this version,
-      e.g. python2-devel.
+      e.g. python3-devel.
 
    .. tab:: Traditional make
 

doc/src/Build_make.rst

@@ -30,9 +30,9 @@ additional tools to be available and functioning.
   * A Bourne shell compatible "Unix" shell program (frequently this is ``bash``)
   * A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
   * Python (optional, required for ``make lib-<pkg>`` in the ``src``
-    folder).  Python scripts are currently tested with python 2.7 and
+    folder).  Python scripts are currently tested with 3.6 to 3.11.
-    3.6 to 3.11. The procedure for :doc:`building the documentation
+    The procedure for :doc:`building the documentation <Build_manual>`
-    <Build_manual>` *requires* Python 3.5 or later.
+    *requires* Python 3.8 or later.
 
 Getting started
 ^^^^^^^^^^^^^^^

doc/src/Build_manual.rst

@@ -162,7 +162,7 @@ are usually installed by default, the following packages are required:
    - dvipng
    - ellipse
    - fncychap
-   - fontawesom
+   - fontawesome
    - framed
    - geometry
    - gyre

doc/src/Intro_portability.rst

@@ -13,10 +13,14 @@ Programming language standards
 
 Most of the C++ code currently requires a compiler compatible with the
 C++11 standard, the KOKKOS package currently requires C++17.  Most of
-the Python code is written to be compatible with Python 3.5 or later or
+the Python code is written to be compatible with Python 3.6 or later.
-Python 2.7.  Some Python scripts *require* Python 3 and a few others
-still need to be ported from Python 2 to Python 3.
 
+.. deprecated:: TBD
+
+Python 2.x is no longer supported and trying to use it, e.g. for the
+LAMMPS Python module should result in an error.  If you come across
+some part of the LAMMPS distribution that is not (yet) compatible with
+Python 3, please notify the LAMMPS developers.
 
 Build systems
 ^^^^^^^^^^^^^
@@ -24,8 +28,8 @@ Build systems
 LAMMPS can be compiled from source code using a (traditional) build
 system based on shell scripts, a few shell utilities (grep, sed, cat,
 tr) and the GNU make program. This requires running within a Bourne
-shell (``/bin/sh``).  Alternatively, a build system with different back ends
+shell (``/bin/sh``).  Alternatively, a build system with different back
-can be created using CMake.  CMake must be at least version 3.16.
+ends can be created using CMake.  CMake must be at least version 3.16.
 
 Operating systems
 ^^^^^^^^^^^^^^^^^

doc/src/Modify_requirements.rst

@@ -189,10 +189,8 @@ of the contribution.  As of January 2023, all previously included
 Fortran code for the LAMMPS executable has been replaced by equivalent
 C++ code.
 
-Python code must be compatible with Python 3.5 and later.  Large parts
+Python code currently must be compatible with Python 3.6.  If a later
-of LAMMPS (including the :ref:`PYTHON package <PKG-PYTHON>`) are also
+version or Python is required, it needs to be documented.
-compatible with Python 2.7.  Compatibility with Python 2.7 is desirable,
-but compatibility with Python 3.5 is **required**.
 
 Compatibility with older programming language standards is very
 important to maintain portability and availability of LAMMPS on many

doc/src/Packages_details.rst

@@ -2428,7 +2428,7 @@ ways to use LAMMPS and Python together.
 
    Building with the PYTHON package assumes you have a Python development
    environment (headers and libraries) available on your system, which needs
-   to be either Python version 2.7 or Python 3.5 and later.
+   to be Python version 3.6 or later.
 
 **Install:**
 

doc/src/Python_install.rst

@@ -7,6 +7,10 @@ LAMMPS shared library through the Python `ctypes <ctypes_>`_
 module.  Because of the dynamic loading, it is required that LAMMPS is
 compiled in :ref:`"shared" mode <exe>`.
 
+.. versionchanged:: TBD
+
+LAMMPS currently only supports Python version 3.6 or later.
+
 Two components are necessary for Python to be able to invoke LAMMPS code:
 
 * The LAMMPS Python Package (``lammps``) from the ``python`` folder
@@ -136,11 +140,6 @@ folder that the dynamic loader searches or inside of the installed
          # create virtual environment in folder $HOME/myenv
          python3 -m venv $HOME/myenv
 
-      For Python versions prior 3.3 you can use `virtualenv
-      <https://packaging.python.org/en/latest/key_projects/#virtualenv>`_
-      command instead of "python3 -m venv".  This step has to be done
-      only once.
-
       To activate the virtual environment type:
 
       .. code-block:: bash
@@ -245,14 +244,14 @@ make MPI calls directly from Python in your script, if you desire.
 We have tested this with `MPI for Python <https://mpi4py.readthedocs.io/>`_
 (aka mpi4py) and you will find installation instruction for it below.
 
-Installation of mpi4py (version 3.0.3 as of Sep 2020) can be done as
+Installation of mpi4py (version 4.0.1 as of Feb 2025) can be done as
 follows:
 
 - Via ``pip`` into a local user folder with:
 
   .. code-block:: bash
 
-     pip install --user mpi4py
+     python3 -m pip install --user mpi4py
 
 - Via ``dnf`` into a system folder for RedHat/Fedora systems:
 
@@ -261,20 +260,20 @@ follows:
      # for use with OpenMPI
      sudo dnf install python3-mpi4py-openmpi
      # for use with MPICH
-     sudo dnf install python3-mpi4py-openmpi
+     sudo dnf install python3-mpi4py-mpich
 
 - Via ``pip`` into a virtual environment (see above):
 
   .. code-block:: console
 
      $ source $HOME/myenv/activate
-     (myenv)$ pip install mpi4py
+     (myenv)$ python -m pip install mpi4py
 
 - Via ``pip`` into a system folder (not recommended):
 
   .. code-block:: bash
 
-     sudo pip install mpi4py
+     sudo python3 -m pip install mpi4py
 
 For more detailed installation instructions and additional options,
 please see the `mpi4py installation <https://mpi4py.readthedocs.io/en/stable/install.html>`_ page.

doc/src/Python_overview.rst

@@ -44,15 +44,11 @@ Below is an example output for Python version 3.8.5.
 .. warning::
 
    The options described in this section of the manual for using Python
-   with LAMMPS currently support either Python 2 or 3.  Specifically
+   with LAMMPS support only Python 3.6 or later.  For use with Python
-   version 2.7 or later and 3.6 or later.  Since the Python community no
+   2.x you will need to use an older LAMMPS version like 29 Aug 2024
-   longer maintains Python 2 (see `this notice
+   or older.  If you notice Python code in the LAMMPS distribution that
-   <https://www.python.org/doc/sunset-python-2/>`_), we recommend use of
+   is not compatible with Python 3, please contact the LAMMPS developers
-   Python 3 with LAMMPS.  While Python 2 code should continue to work,
+   or submit `and issue on GitHub <https://github.com/lammps/lammps/issues>`_
-   that is not something we can guarantee long-term.  If you notice
-   Python code in the LAMMPS distribution that is not compatible with
-   Python 3, please contact the LAMMPS developers or submit `and issue
-   on GitHub <https://github.com/lammps/lammps/issues>`_
 
 ---------
 

doc/src/region2vmd.rst

@@ -166,11 +166,7 @@ Only the following region styles are currently supported: *block*,
 *cone*, *cylinder*, *ellipsoid*, *prism*, and *sphere*. Regions formed
 from unions or intersections of other regions are not supported.
 
-For region style *cone* one of the two radii must be zero, since the
+Rotating regions are currently not supported.
-equivalent VMD graphics primitive does not support truncated cones.
-Also the VMD graphics primitive does not support open cones.
-
-Rotating regions are not supported.
 
 Related commands
 """"""""""""""""

doc/utils/sphinx-config/false_positives.txt

@@ -99,6 +99,7 @@ AMD
 amino
 Amirjalayer
 Amit
+amsmath
 amu
 Amzallag
 analytical
@@ -128,6 +129,7 @@ Antisymmetrized
 antisymmetry
 anton
 Antonelli
+anysize
 api
 apolar
 Apoorva
@@ -613,6 +615,7 @@ Courant
 covalent
 covalently
 covariance
+cp
 cpp
 cpu
 cradius
@@ -905,6 +908,7 @@ dUs
 Duval
 dV
 dvector
+dvipng
 dVx
 dW
 dx
@@ -1215,12 +1219,14 @@ fmz
 fN
 Fn
 fname
+fncychap
 fno
 Fnudge
 foces
 Fock
 Fogarty
 Foiles
+fontawesome
 fopenmp
 forceclear
 forestgreen
@@ -1407,6 +1413,7 @@ Gunsteren
 Gunzenmuller
 Guo
 gw
+gyre
 gyromagnetic
 gz
 gzip
@@ -1532,10 +1539,12 @@ hydrostatically
 hydroxyl
 Hynninen
 Hyoungki
+hypcap
 hyperdynamics
 hyperparameters
 hyperplane
 hyperradius
+hyperref
 hyperspherical
 hysteretic
 hz
@@ -2514,6 +2523,7 @@ Ndof
 Ndouble
 ndx
 neb
+needspace
 neel
 Neel
 Neelov
@@ -2918,6 +2928,7 @@ picogram
 picograms
 picosecond
 picoseconds
+pict
 pid
 piecewise
 Pieniazek
@@ -3689,6 +3700,7 @@ Sz
 Tabbernor
 tabinner
 tabstyle
+tabulary
 Tadmor
 Tafipolsky
 tagID
@@ -3786,6 +3798,7 @@ timestamps
 timestep
 timestepping
 timesteps
+titlesec
 TiN
 TiO
 Tirado
@@ -3962,6 +3975,7 @@ untilted
 Unwin
 uparrow
 upenn
+upquote
 upto
 Urbakh
 Urbana
@@ -4148,6 +4162,7 @@ Workum
 Worley
 wormlike
 wpbe
+wrapfig
 Wriggers
 writedata
 Wuppertal
@@ -4178,6 +4193,7 @@ Xia
 Xiaohu
 Xiaowang
 Xie
+xindy
 xk
 xlat
 xlattice

lib/python/Makefile.lammps.python2

@@ -1,7 +0,0 @@
-# Settings that the LAMMPS build will import when this package library is used
-# See the README file for more explanation
-
-python_SYSINC = $(shell which python2-config > /dev/null 2>&1 && python2-config --includes || (which python-config > /dev/null 2>&1 && python-config --includes || :))
-python_SYSLIB = $(shell which python2-config > /dev/null 2>&1 && python2-config --ldflags || (which python-config > /dev/null 2>&1 && python-config --ldflags || :))
-python_SYSPATH =
-PYTHON=$(shell which python2 > /dev/null 2>&1 && echo python2 || echo python)

lib/python/README

@@ -9,30 +9,29 @@ installation. If needed, you can copy one of the other provided
 Makefile.lammps.* files to to Makefile.lammps before building
 LAMMPS itself.
 
-The files Makefile.lammps.python2 and Makefile.lammps.python3 are
+The file Makefile.lammps.python3 is similar to the default file, but
-similar to the default file, but meant for the case that both,
+meant for the case that both, python 2 and python 3, are installed
-python 2 and python 3, are installed simultaneously and you want
+simultaneously.  LAMMPS only supports python 3.  If neither of these
-to prefer one over the other. If neither of these files work, you
+files work, you may have to create a custom Makefile.lammps file
-may have to create a custom Makefile.lammps file suitable for
+suitable for the version of Python on your system.  To illustrate, these
-the version of Python on your system.  To illustrate, these are
+are example settings from the Makefile.lammps.python3.13 file:
-example settings from the Makefile.lammps.python2.7 file:
 
-python_SYSINC = -I/usr/local/include/python2.7
+python_SYSINC = -I/usr/local/include/python3.13
-python_SYSLIB = -lpython2.7 -lnsl -ldl -lreadline -ltermcap -lpthread -lutil -lm
+python_SYSLIB = -lpython3.13 -ldl  -lm
-python_SYSPATH =
+python_SYSPATH = -L/usr/lib64
-PYTHON=python2.7
+PYTHON=python3.13
 
 python_SYSINC refers to the directory where Python's Python.h file is
 found.  LAMMPS includes this file.
 
 python_SYSLIB refers to the libraries needed to link to from an
 application (LAMMPS in this case) to "embed" Python in the
-application.  The Python library itself is listed (-lpython2.7) are
+application.  The Python library itself is listed (-lpython3.13) are
 are several system libraries needed by Python.
 
 python_SYSPATH refers to the path (e.g. -L/usr/local/lib) where the
 Python library can be found.  You may not need this setting if the
-path is already included in your LD_LIBRARY_PATH environment variable.
+path is already included in your LIBRARY_PATH environment variable.
 
 PYTHON is the name of the python interpreter. It is used for
 installing the LAMMPS python module with "make install-python"
@@ -45,7 +44,7 @@ run in embedded mode on your machine.
 
 Here is what this Python doc page says about it:
 
-https://docs.python.org/2/extending/embedding.html#compiling-and-linking-under-unix-like-systems
+https://docs.python.org/3/extending/embedding.html#compiling-and-linking-under-unix-like-systems
 
 "It is not necessarily trivial to find the right flags to pass to your
 compiler (and linker) in order to embed the Python interpreter into

python/README

@@ -1,20 +1,27 @@
-This directory contains Python code which wraps LAMMPS as a library
+This directory contains the LAMMPS Python module that allows the LAMMPS
-and allows the LAMMPS library interface to be invoked from Python,
+C library interface to be invoked from Python, either from a Python
-either from a Python script or using Python interactively.
+script or using Python interactively.
 
 Details on the Python interface to LAMMPS and how to build LAMMPS as a
 shared library, for use with Python, are given in
-doc/Section_python.html and in doc/Section_start.html#start_5.
+https://docs.lammps.org/Build_basics.html#exe
+and
+https://docs.lammps.org/Python_install.html
 
-Basically you need to follow these steps in the src directory:
+Basically you need to use the flag -D BUILD_SHARED_LIBS=ON when
+configuring LAMMPS with CMake and then in the build folder use the
+command % cmake --build . --target install-python
+
+or for the legacy GNU build system execute these steps in the src folder:
 
 % make g++ mode=shlib           # build for whatever machine target you wish
 % make install-python           # install into site-packages folder
 
 You can replace the last step by a one-time setting of environment
-variables in your shell script.  Or you can run the python/install.py
+variables in your shell environment.  Or you can run the
-script directly to give you more control over where the two relevant
+python/install.py script directly to give you more control over where
-files are installed.  See doc/Python_install.html for details.
+the two relevant files are installed.  See
+https://docs.lammps.org/Python_install.html for details.
 
 You should then be able to launch Python and instantiate an instance
 of LAMMPS:
@@ -24,39 +31,41 @@ of LAMMPS:
 >>> lmp = lammps()
 
 If that gives no errors, you have successfully wrapped LAMMPS with
-Python.  See doc/Section_python.html#py_7 for tests you can then use
+Python.  See https://docs.lammps.org/Python_launch.html for examples how
-to run LAMMPS both in serial or parallel thru Python.
+to run LAMMPS both in serial or parallel from Python.
 
 Note that you can also invoke Python code from within a LAMMPS input
-script, using the "python" command.  See the doc/python.html doc page
+script, using the "python" command.  See the
-for details.  The Python code you invoke can also call back to LAMMPS
+https://docs.lammps.org/python.html doc page for details.  The Python
-using the same interface described here for wrapping LAMMPS.
+code you invoke can also call back to LAMMPS using the same interface
+described here for wrapping LAMMPS.
 
 -------------------------------------------------------------------
 
 Once you have successfully wrapped LAMMPS, you can run the Python
 scripts in the examples sub-directory:
 
-trivial.py          read/run a LAMMPS input script thru Python
+trivial.py            read/run a LAMMPS input script thru Python
-demo.py             invoke various LAMMPS library interface routines
+demo.py               invoke various LAMMPS library interface routines
-simple.py           parallel example, mimicing examples/COUPLE/simple/simple.cpp
+simple.py             parallel example, mimicing examples/COUPLE/simple/simple.cpp
-split.py            parallel example
+split.py              parallel example
-mc.py               Monte Carlo energy relaxation wrapper on LAMMPS
+mc.py                 Monte Carlo energy relaxation wrapper on LAMMPS
-gui.py              GUI go/stop/temperature-slider to control LAMMPS
+gui.py                GUI go/stop/temperature-slider to control LAMMPS
-plot.py             real-time temperature plot with GnuPlot via Pizza.py
+plot.py               real-time temperature plot with GnuPlot via Pizza.py
-matplotlib_plot.py  real-time temperature plot with Matplotlib via Pizza.py
+matplotlib_plot.py    real-time temperature plot with Matplotlib via Pizza.py
-viz_tool.py         real-time viz via some viz package
+viz_<tool>.py         real-time viz via some viz package
-vizplotgui_tool.py  combination of viz.py and plot.py and gui.py
+vizplotgui_<tool>.py  combination of viz.py and plot.py and gui.py
 
-For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
+For the viz_<tool>.py and vizplotgui_<tool>.py commands, replace
-with "gl" or "atomeye" or "pymol", depending on what visualization
+"<tool>" with "gl" or "atomeye" or "pymol", depending on what
-package you have installed.  We hope to add a VMD option soon.
+visualization package you have installed.  We hope to add a VMD option
+soon.
 
 Note that for GL, you need to be able to run the Pizza.py GL tool,
 which is included in the pizza sub-directory.  See the Pizza.py doc
 pages for more info:
 
-http://www.sandia.gov/~sjplimp/pizza.html
+https://lammps.github.io/pizza/
 
 Note that for AtomEye, you need version 3, and their is a line in the
 scripts that specifies the path and name of the executable.  See
@@ -115,17 +124,14 @@ one-processor run, where both Python and LAMMPS will run on single
 processors.  Each running job will read the same input file, and write
 to same log.lammps file, which isn't too useful.
 
-However, if you have the mpi4py Python package installed and uncomment mpi4py
+However, if you have the mpi4py Python package installed and uncomment
-code in simple.py, then the above commands will invoke 1 instance of a
+mpi4py code in simple.py, then the above commands will invoke 1 instance
-P-processor run.  Both Python and LAMMPS will run on P processors.  The job will
+of a P-processor run.  Both Python and LAMMPS will run on P processors.
-read the input file and write a single log.lammps file.
+The job will read the input file and write a single log.lammps file.
-
-The split.py script can also be run in parallel.  It uses mpi4py
-version 2.0.0 (or later), which makes it possible to pass a
-communicator when creating the LAMMPS object and thus run multiple
-instances of LAMMPS at the same time, each on a different subset of
-MPI ranks.  Or run LAMMPS on one subset and some other program on the
-rest of the MPI ranks, concurrently.  See comments in the split.py
-script for more details.
-
 
+The split.py script can also be run in parallel.  It uses mpi4py version
+2.0.0 (or later), which makes it possible to pass a communicator when
+creating the LAMMPS object and thus run multiple instances of LAMMPS at
+the same time, each on a different subset of MPI ranks.  Or run LAMMPS
+on one subset and some other program on the rest of the MPI ranks,
+concurrently.  See comments in the split.py script for more details.

python/lammps/__init__.py

@@ -23,6 +23,9 @@ def get_version_number():
     if __file__.find(join('python', 'lammps', '__init__.py')) > 0:
         return 0
 
+    if version_info.major < 3 or (version_info.major == 3 and version_info.minor < 6):
+        raise SystemError('LAMMPS only supports Python version 3.6 or later')
+
     vstring = None
     if version_info.major == 3 and version_info.minor >= 8:
         from importlib.metadata import version, PackageNotFoundError

python/lammps/core.py

@@ -83,8 +83,6 @@ class command_wrapper(object):
 
   def _wrap_args(self, x):
       if callable(x):
-          if sys.version_info <  (3,):
-            raise Exception("Passing functions or lambdas directly as arguments is only supported in Python 3 or newer")
           import hashlib
           import __main__
           sha = hashlib.sha256()
@@ -105,11 +103,6 @@ class command_wrapper(object):
     all the arguments, concatinates them to a single string, and executes it using
     :py:meth:`lammps.command`.
 
-    Starting with Python 3.6 it also supports keyword arguments. key=value is
-    transformed into 'key value'. Note, since these have come last in the
-    parameter list, only a subset of LAMMPS commands can be used with this
-    syntax.
-
     LAMMPS commands that accept callback functions (such as fix python/invoke)
     can be passed functions and lambdas directly. The first argument of such
     callbacks will be an lammps object constructed from the passed LAMMPS
@@ -121,9 +114,6 @@ class command_wrapper(object):
     def handler(*args, **kwargs):
       cmd_args = [name] + [str(self._wrap_args(x)) for x in args]
 
-      if len(kwargs) > 0 and sys.version_info < (3,6):
-         raise Exception("Keyword arguments are only supported in Python 3.6 or newer")
-
       # Python 3.6+ maintains ordering of kwarg keys
       for k in kwargs.keys():
           cmd_args.append(k)
@@ -530,16 +520,10 @@ class lammps(object):
 
     else:
       # magic to convert ptr to ctypes ptr
-      if sys.version_info >= (3, 0):
+      # Python 3 (uses PyCapsule API)
-        # Python 3 (uses PyCapsule API)
+      pythonapi.PyCapsule_GetPointer.restype = c_void_p
-        pythonapi.PyCapsule_GetPointer.restype = c_void_p
+      pythonapi.PyCapsule_GetPointer.argtypes = [py_object, c_char_p]
-        pythonapi.PyCapsule_GetPointer.argtypes = [py_object, c_char_p]
+      self.lmp = c_void_p(pythonapi.PyCapsule_GetPointer(ptr, None))
-        self.lmp = c_void_p(pythonapi.PyCapsule_GetPointer(ptr, None))
-      else:
-        # Python 2 (uses PyCObject API)
-        pythonapi.PyCObject_AsVoidPtr.restype = c_void_p
-        pythonapi.PyCObject_AsVoidPtr.argtypes = [py_object]
-        self.lmp = c_void_p(pythonapi.PyCObject_AsVoidPtr(ptr))
 
     # check if library initilialization failed
     if not self.lmp:

src/KOKKOS/mliap_model_python_kokkos.cpp

@@ -68,12 +68,12 @@ MLIAPModelPythonKokkos<DeviceType>::MLIAPModelPythonKokkos(LAMMPS *lmp, char *co
   // Recipe from lammps/src/pair_python.cpp :
   // add current directory to PYTHONPATH
   PyObject *py_path = PySys_GetObject((char *) "path");
-  PyList_Append(py_path, PY_STRING_FROM_STRING("."));
+  PyList_Append(py_path, PyUnicode_FromString("."));
 
   // if LAMMPS_POTENTIALS environment variable is set, add it to PYTHONPATH as well
   const char *potentials_path = getenv("LAMMPS_POTENTIALS");
   if (potentials_path != nullptr) {
-    PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path));
+    PyList_Append(py_path, PyUnicode_FromString(potentials_path));
   }
   PyGILState_Release(gstate);
   if (coefffilename) read_coeffs(coefffilename);

src/ML-IAP/mliap_model_python.cpp

@@ -62,12 +62,12 @@ MLIAPModelPython::MLIAPModelPython(LAMMPS *lmp, char *coefffilename, bool is_chi
   // Recipe from lammps/src/pair_python.cpp :
   // add current directory to PYTHONPATH
   PyObject *py_path = PySys_GetObject((char *) "path");
-  PyList_Append(py_path, PY_STRING_FROM_STRING("."));
+  PyList_Append(py_path, PyUnicode_FromString("."));
 
   // if LAMMPS_POTENTIALS environment variable is set, add it to PYTHONPATH as well
   const char *potentials_path = getenv("LAMMPS_POTENTIALS");
   if (potentials_path != nullptr) {
-    PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path));
+    PyList_Append(py_path, PyUnicode_FromString(potentials_path));
   }
   PyGILState_Release(gstate);
   if (coefffilename) read_coeffs(coefffilename);

src/Makefile

@@ -2,6 +2,12 @@
 
 SHELL = /bin/bash
 PYTHON = python
+PYTHON_VERSION=$(word 2,$(shell $(PYTHON) -V 2>&1 | tr '.' ' '))
+ifeq ($(PYTHON_VERSION),2)
+PYTHON_CHECK=@echo LAMMPS requires Python 3. Try: 'make PYTHON=python3 ...' ; exit 1
+else
+PYTHON_CHECK=@echo
+endif
 DYN_LIB = -ldl
 
 #.IGNORE:
@@ -276,7 +282,7 @@ LIBDIR = $(@:lib-%=%)
 # List of all targets
 
 help:
-	@echo ''
+	$(PYTHON_CHECK)
 	@echo 'make clean-all           delete all object files'
 	@echo 'make clean-machine       delete object files for one machine'
 	@echo 'make mpi-stubs           build dummy MPI library in STUBS'
@@ -378,6 +384,7 @@ gitversion:
 # shared = shared compile in Obj_shared_machine
 
 .DEFAULT:
+	$(PYTHON_CHECK)
 	@if [ $@ = "serial" ]; \
 	  then cd STUBS; $(MAKE); cd ..; fi
 	@test -f MAKE/Makefile.$@ -o -f MAKE/OPTIONS/Makefile.$@ -o \
@@ -465,6 +472,7 @@ mpi-stubs:
 
 sinclude ../lib/python/Makefile.lammps
 install-python:
+	$(PYTHON_CHECK)
 	@rm -rf ../python/build
 	@$(PYTHON) ../python/install.py -p ../python/lammps -l ../src/liblammps.so -w $(PWD) -v $(PWD)/version.h
 
@@ -483,49 +491,59 @@ tar:
 check: check-whitespace check-permissions check-homepage check-errordocs check-fmtlib check-docs check-version
 
 check-whitespace:
+	$(PYTHON_CHECK)
 	$(PYTHON) ../tools/coding_standard/whitespace.py ..
 
 fix-whitespace:
+	$(PYTHON_CHECK)
 	$(PYTHON) ../tools/coding_standard/whitespace.py .. -f
 
 check-permissions:
+	$(PYTHON_CHECK)
 	$(PYTHON) ../tools/coding_standard/permissions.py ..
 
 fix-permissions:
+	$(PYTHON_CHECK)
 	$(PYTHON) ../tools/coding_standard/permissions.py .. -f
 
 check-homepage:
+	$(PYTHON_CHECK)
 	$(PYTHON) ../tools/coding_standard/homepage.py ..
 
 fix-homepage:
+	$(PYTHON_CHECK)
 	$(PYTHON) ../tools/coding_standard/homepage.py .. -f
 
 check-errordocs:
+	$(PYTHON_CHECK)
 	$(PYTHON) ../tools/coding_standard/errordocs.py ..
 
 fix-errordocs:
+	$(PYTHON_CHECK)
 	$(PYTHON) ../tools/coding_standard/errordocs.py .. -f
 
 check-fmtlib:
+	$(PYTHON_CHECK)
 	$(PYTHON) ../tools/coding_standard/fmtlib.py ..
 
 fix-fmtlib:
+	$(PYTHON_CHECK)
 	$(PYTHON) ../tools/coding_standard/fmtlib.py .. -f
 
 check-docs:
+	$(PYTHON_CHECK)
 	$(MAKE) $(MFLAGS) -C ../doc anchor_check style_check package_check role_check
 
 check-version:
+	$(PYTHON_CHECK)
 	$(PYTHON) ../tools/coding_standard/versiontags.py .. || echo
 
-
 format-src:
 	clang-format -i --verbose --style=file *.cpp *.h */*.cpp */*.h
 
 format-tests:
 	clang-format -i --verbose --style=file ../unittest/*/*.cpp ../unittest/*/*.h
 
-
 # Package management
 
 package:

src/PYTHON/fix_python_invoke.cpp

@@ -70,7 +70,7 @@ FixPythonInvoke::FixPythonInvoke(LAMMPS *lmp, int narg, char **arg) :
     error->all(FLERR,"Could not find Python function");
   }
 
-  lmpPtr = PY_VOID_POINTER(lmp);
+  lmpPtr = PyCapsule_New((void *)lmp, nullptr, nullptr);
 
   // nvalid = next step on which end_of_step or post_force does something
   // add nextvalid() to all computes that store invocation times

src/PYTHON/fix_python_move.cpp

@@ -44,7 +44,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
 
   // add current directory to PYTHONPATH
   PyObject *py_path = PySys_GetObject((char *)"path");
-  PyList_Append(py_path, PY_STRING_FROM_STRING("."));
+  PyList_Append(py_path, PyUnicode_FromString("."));
 
 
   // create integrator instance
@@ -73,7 +73,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
     error->all(FLERR,"Could not find integrator class {} in module {}", cls_name, module_name);
   }
 
-  PyObject *ptr = PY_VOID_POINTER(lmp);
+  PyObject *ptr = PyCapsule_New((void *)lmp, nullptr, nullptr);
   PyObject *py_move_obj = PyObject_CallFunction(py_move_type, (char *)"O", ptr);
   Py_CLEAR(ptr);
 

src/PYTHON/pair_python.cpp

@@ -54,14 +54,14 @@ PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
 
   PyUtils::GIL lock;
   PyObject *py_path = PySys_GetObject((char *)"path");
-  PyList_Append(py_path, PY_STRING_FROM_STRING("."));
+  PyList_Append(py_path, PyUnicode_FromString("."));
 
   // if LAMMPS_POTENTIALS environment variable is set,
   // add it to PYTHONPATH as well
 
   const char *potentials_path = getenv("LAMMPS_POTENTIALS");
   if (potentials_path != nullptr) {
-    PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path));
+    PyList_Append(py_path, PyUnicode_FromString(potentials_path));
   }
 }
 

src/PYTHON/python_compat.h

@@ -16,22 +16,11 @@
 
 #include <Python.h>
 
-// Wrap API changes between Python 2 and 3 using macros
+#if PY_VERSION_HEX < 0x030600f0
-#if PY_MAJOR_VERSION == 2
+#error Python version 3.6 or later is required by LAMMPS
-#if defined(_MSC_VER) || defined(__MINGW32__)
-#define PY_INT_FROM_LONG(X) PyLong_FromLongLong(X)
-#define PY_INT_AS_LONG(X) PyLong_AsLongLong(X)
-#define PY_LONG_FROM_STRING(X) std::stoll(X)
-#else
-#define PY_INT_FROM_LONG(X) PyInt_FromLong(X)
-#define PY_INT_AS_LONG(X) PyInt_AsLong(X)
-#define PY_LONG_FROM_STRING(X) std::stol(X)
 #endif
-#define PY_STRING_FROM_STRING(X) PyString_FromString(X)
-#define PY_VOID_POINTER(X) PyCObject_FromVoidPtr((void *) X, nullptr)
-#define PY_STRING_AS_STRING(X) PyString_AsString(X)
 
-#elif PY_MAJOR_VERSION == 3
+// Wrap API differences between platforms using macros
 #if defined(_MSC_VER) || defined(__MINGW32__)
 #define PY_INT_FROM_LONG(X) PyLong_FromLongLong(X)
 #define PY_INT_AS_LONG(X) PyLong_AsLongLong(X)
@@ -41,9 +30,5 @@
 #define PY_INT_AS_LONG(X) PyLong_AsLong(X)
 #define PY_LONG_FROM_STRING(X) std::stol(X)
 #endif
-#define PY_STRING_FROM_STRING(X) PyUnicode_FromString(X)
-#define PY_VOID_POINTER(X) PyCapsule_New((void *) X, nullptr, nullptr)
-#define PY_STRING_AS_STRING(X) PyUnicode_AsUTF8(X)
-#endif
 
 #endif

src/PYTHON/python_impl.cpp

@@ -361,12 +361,12 @@ void PythonImpl::invoke_function(int ifunc, char *result)
         if (!str)
           error->all(FLERR, "Could not evaluate Python function {} input variable: {}",
                      pfuncs[ifunc].name, pfuncs[ifunc].svalue[i]);
-        pValue = PY_STRING_FROM_STRING(str);
+        pValue = PyUnicode_FromString(str);
       } else {
-        pValue = PY_STRING_FROM_STRING(pfuncs[ifunc].svalue[i]);
+        pValue = PyUnicode_FromString(pfuncs[ifunc].svalue[i]);
       }
     } else if (itype == PTR) {
-      pValue = PY_VOID_POINTER(lmp);
+      pValue = PyCapsule_New((void *)lmp, nullptr, nullptr);
     } else {
       error->all(FLERR, "Unsupported variable type: {}", itype);
     }
@@ -397,7 +397,7 @@ void PythonImpl::invoke_function(int ifunc, char *result)
       auto value = fmt::format("{:.15g}", PyFloat_AsDouble(pValue));
       strncpy(result, value.c_str(), Variable::VALUELENGTH - 1);
     } else if (otype == STRING) {
-      const char *pystr = PY_STRING_AS_STRING(pValue);
+      const char *pystr = PyUnicode_AsUTF8(pValue);
       if (pfuncs[ifunc].longstr)
         strncpy(pfuncs[ifunc].longstr, pystr, pfuncs[ifunc].length_longstr);
       else

src/safe_pointers.h

@@ -17,6 +17,7 @@
 // collection of smart pointers for specific purposes
 
 #include <cstdio>
+#include <utility>
 
 namespace LAMMPS_NS {
 
@@ -36,7 +37,7 @@ class SafeFilePtr {
   SafeFilePtr(FILE *_fp) : fp(_fp) {};
 
   SafeFilePtr(const SafeFilePtr &) = delete;
-  SafeFilePtr(const SafeFilePtr &&) = delete;
+  SafeFilePtr(SafeFilePtr &&o) noexcept : fp(std::exchange(o.fp, nullptr)) {}
   SafeFilePtr &operator=(const SafeFilePtr &) = delete;
 
   ~SafeFilePtr()